


Bridges Burned

by AngelQueen



Category: Stargate Atlantis
Genre: Alternate Universe - Canon, Angst, Challenge Response, F/M
Language: English
Status: Completed
Published: 2011-04-09
Updated: 2011-04-09
Packaged: 2017-10-17 20:26:57
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 5,008
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/180876
Author URL: https://archiveofourown.org/users/AngelQueen/pseuds/AngelQueen
Summary: <blockquote class="userstuff">
              <p>Someone <i>else</i> saves the day, and it opens up the can of worms from hell.</p>
            </blockquote>





	Bridges Burned

**Author's Note:**

> Written for the 2009 S4/S5 Fix It Challenge at john_elizabeth (http://community.livejournal.com/john_elizabeth).
> 
>  **Disclaimer:** SGA does not belong to me.

The first time they had endured a Wraith siege, McKay had said that the constant bombardment against Atlantis’ shield was almost pretty. Sheppard hadn’t agreed with him then, and he disagreed even more so now.

They’d been on New Lantea for less than a year and it looked like they weren’t going to be able to stay. At least one Wraith hive ship knew about them. Atlantis’ sensors hadn’t picked up any other cruisers coming this way, but it was possible they had informed others. When – if – they had dealt with this cruiser, they were going to have to discuss new arrangements.

* * *

The stars were unfamiliar here. It had taken her nearly three years to get used to the stars in Pegasus, how they had appeared on the horizon and how different they were from what she had been used to. She knew these stars were many of the same ones she had come to know, but their configuration was different. It just didn’t feel quite right.

 _Wraith power output at eighty-eight percent. For maximum damage to occur, power output must be at fifty-five percent or lower. Intervention not recommended at this time._

She tensed and looked away from the stars. She was here for a purpose, and it wasn’t to stargaze. She just had to wait for the right moment to strike. Once the power output was at the right level, they could strike and not have to worry about fending off a counterattack.

* * *

The ZPM’s power was still holding out, but they knew from experience that it couldn’t hold out indefinitely to a continued Wraith assault. Even sinking the city beneath the ocean would only buy them a few hours, a day at most. They had the puddlejumpers, which could be used to make a run against the hive ship, but to get them out there they would have to drop the shield, which would be bad, very bad.

Sam had ordered an evacuation of all nonessential personnel through the Stargate to one of the Alpha sites, where they could send a signal to the _Daedalus_ when it reentered Pegasus. Teyla had gone with them, knowing she would do no good in the city in her current condition, but had still been reluctant to leave her friends. John had ordered Ronon to shove her through the Gate if she put up too much of a fight. He wouldn’t have a baby’s death on his conscience.

* * *

 _Wraith power output at sixty-seven percent. For maximum damage to occur, power output must be at fifty-five percent or lower. Intervention not recommended at this time._

 _Soon,_ she thought. Just a few more seconds.

* * *

“Drones might, I repeat, _might_ get through their shields, but the darts will probably just intercept most of them. Not enough of them will get through to do any kind of real damage!”

John shifted his glare from the shield. “Get to the point, McKay,” he snapped.

“That is the point!” McKay shrilled. “We are _screwed_! Completely –”

Then things changed. They _weren’t_ screwed.

* * *

 _Wraith power output at fifty-five percent. Maximum damage now possible. Intervention recommended at this time._

 _Yes._ Now she could safely intervene, now she could save her city without endangering her people.

The irony of that statement was not lost on her.

* * *

The ship appeared out of nowhere. One minute the Wraith hive sat in orbit alone, firing without pause down on the surface where Atlantis stood. The city’s life expectancy was measured in hours.

By the time McKay began shouting about another ship appearing in orbit, it was practically over. The red hue that had permeated the city since the attack had begun vanished, replaced by the normal blue tinge from the ocean.

John stared at McKay over the sensor equipment. “Who the hell is that?”

“Scanning,” Rodney answered briskly. His eyes widened and he looked up. “It’s a Replicator ship.”

John inhaled sharply, but Sam spoke up. “Should we put up the cloak?”

He shook his head. “It won’t matter,” John told her. “They’ve already got a fix on our position. If they want to blow us to hell, it won’t take ‘em long.” He turned back to Rodney. “What are they doing now?”

“They’re just sitting there. Their weapons are still powered, but they aren’t moving any closer.”

So that left a fair share of questions. What now? Why had a Replicator ship gotten involved? Why hadn’t they just helped blow Atlantis straight to hell before taking out the Wraith? If they wanted to take out the Wraith first, why weren’t they firing on the city? With weapons that were Ancient-based, it wouldn’t take more than few minutes to drain the ZPM powering the shield and blow the city sky high.

“Maybe,” Rodney suggested in the snide tone he used when he firmly believed all the people around him were morons, “we should try talking to them?”

* * *

 _Wraith hive ship destroyed. No damage to any systems. Element of surprise enabled positive outcome of venture._

There. It was done. Now –

 _Communication signal incoming, originating from the location of Atalantë. Open channel?_

Silence. She had known this was a possibility, them contacting her before she could make good her getaway. She hadn’t had an answer for what she’d do before, and she didn’t know now.

What needed to be said, really? Their actions had spoken for themselves. But once not so very long ago, she had loved every resident of that city…

 _Orders, Commander?_

 _Fine, open the damn channel. We will not stay long._

* * *

Sam called over an open channel, asking for a dialogue with the Replicator, and for several moments, there was no response. John held his breath, and he was pretty sure Ronon and Rodney were doing the same.

“I repeat,” Sam continued, “this is Atlantis. Will you –”

The sound of static cut her off, and was then replaced by a single voice.

 _“Atlantis, this is Weir.”_

John was pretty sure his heart stopped and slid right up into his throat. He couldn’t believe it. _She_ was here? How? Eliz–

 _“We have been tracking that hive ship for several weeks, monitoring its movements and communications with other groups. There has been no collaboration on their part to attack Atlantis, so I believe your location died with them.”_

John’s hand clenched the console in front of him while he tried to steady his breathing. _It’s not possible…_

 _“However, we are uncertain as to how they divined your location. I would suggest in the future that you take more care when you are dialing Atlantis.”_ Her tone was scathing. Sheppard winced.

Rodney wasn’t so tongue-tied. “E-Elizabeth?”

 _“Our assistance appears to be no longer needed. We will take our leave.”_

“No!” It had taken those words to make Sheppard find his voice. “Elizabeth, wait!”

There was a pause for several seconds, but he knew that the channel had not been closed. Still, the response was not what he had hoped for.

 _“Colonel Sheppard.”_ If anything, her voice was even more frigid than before.

“What’s your hurry?” he asked, trying to sound flippant. He doubted anyone was fooled by it. “We appreciate the help. Give us a little time and we’ll break out the cake and –”

 _“Our presence here is no longer required,”_ she cut him off abruptly, _“but there are other hive ships that we have been tracking that must be dealt with before they attempt to cull some of the more populated worlds. Please try to keep the city intact. I may not be here to save it a third time.”_

* * *

 _Hyperspace engines are charged. Coordinates have been set into the navigation systems._

She had no concrete reason to stay, and she knew that if she didn’t leave now she never would. The city… it still called to her, still made her heart sing. She wanted to see it again, had dreamed about it repeatedly, but she also knew of the treatment she would receive if she went down there. _They_ would never trust her, and she couldn’t risk trusting them. Not again.

 _Good. Let’s go._

* * *

They couldn’t go after her immediately, of course. There was far too much to do. They had to recall the expedition from the Alpha site, alert the _Daedalus_ and Earth that Atlantis had yet again dodged the fatal bullet, and clean up the mess the battle had left behind. Rodney was very particular about repairs done, and barely trusted Zelenka to run diagnostics, much less do serious circuit work on anything.

Nonetheless, John’s brain was only partially engaged by work. The other half kept running the entire scene in his mind, asking the same questions over and over.

 _How is she alive? Why did the Replicator version lie? Why_ would _she lie? Why didn’t she stay? Didn’t she want to see them, see the city?_

Guilt had been his constant companion for years, that was nothing new. With what had happened to Elizabeth, though, that was different. The ache that had John had always lived with suddenly became full-out pain. He had become complacent, and Elizabeth had paid the price. He had always thought that on Atlantis, she was safe, that nothing could harm her while she was here. He had forgotten the lesson that Kolya, that Phoebus and Thalan, had taught him. There was no place that was completely safe.

He had failed her. Maybe now, though, he had a chance to make it up to her, to _apologize_.

Once the expedition was safely back in Atlantis and people heard that they’d been saved by a Replicator ship bearing _Elizabeth_ of all people, it was like a fire had been lit under everyone’s collective asses. Sheppard was pretty sure that everyone had the same thought, of finding her and thanking her and _getting her to come home_. So it was no surprise that, once everything was cleaned up, practically every team stepped forward when Sam asked for volunteers to go on the search for Elizabeth and her ship.

They didn’t find much of anything at first. The odd rumor here and there of Wraith technology being sold for scrap, nothing solid. John knew that finding a woman who didn’t seem inclined to be found wasn’t going to be easy, which didn’t improve his mood or that of any of the others who were involved in the search.

It was Lorne’s team that got the first break. On a trip to Manaria, they were quickly apprised of amazed tales of a Wraith hive ship being destroyed right as it settled into orbit and even before the darts came down to cull. As luck would have it, there had also been a Traveler ship present that had left soon after and the captain had supposedly spoken with the leader of the Wraith Killers.

After that, things got a little easier. One of the Manarians could to contact the Traveler ship as he had been doing business with them for a long time, and agreed to do so for the Atlanteans. For a price of course. John was then introduced to Katana Labrea, who had apparently heard of him from Larrin. From the smirk on the woman’s face, he could only imagine what the blonde brat had told her.

On the subject of the Wraith Killers, Labrea was a veritable gold mine of information. She had spoken to the captain of the ship, which she had recognized as a Replicator vessel, and had been assured that their only intention was to hunt Wraith and possibly forge the occasional alliance. Labrea had described the woman as a great diplomat, which was enough of a giveaway alone for John, but had also described her as a pretty woman with dark curly hair and a smirk that made Labrea’s first officer weak at the knees.

“That’s her,” John had muttered.

After clearing it with Sam, John asked Labrea to ferry him and his team to their next scheduled meeting with Elizabeth’s ship, which was apparently called the _Aeneid_ , of all things.

Labrea had hesitated. “I don’t know,” she said, “they’re a bit jumpy about talking to people. The only reason they kept talking to me was because I was a trader. I don’t want to jeopardize this alliance, it means too much to my people.”

John had opened his mouth to reply, his frustration mounting, but luckily, Teyla headed him off. “We understand, Captain,” she had said quietly, “and normally we would not ask you to take such a risk, but this is a matter very dear to our hearts. Commander Weir, as you call her, was once one of our people.”

Labrea’s dark eyebrows had risen. “Really?”

“Yes,” Teyla had nodded. “She was our leader, and our dear friend. She was taken from us by the Replicators, and some time ago we received intelligence that they had killed her. To know that she is alive has brought great hope to us all.” One of her hands fluttered down to her rounded stomach. “Much has changed since she has been away, much we would want her to know.”

For a moment, Labrea had stared at them, likely weighing her options. Finally, she sighed. “All right,” she said, “I’ll take you. Just… don’t make me regret this.”

The trip took three days, and when they came out of hyperspace, they found themselves at a lush, uninhabited planet. A familiar ship was in orbit.

John took a deep breath. It was time to go.

* * *

 _Captain Labrea, human, requests an audience. She is accompanied by four attendants. They are not dressed like her crew, however._

She looked up from her work, mildly alarmed. _Are they armed?_

 _Yes. One has an energy-based weapon, the other three carry the firearms of the humans from Atalantë._

Something in her froze. She had expected that they would go looking for her, if only to determine her threat level to them, but she had not thought they would actually _find_ her.

She sighed. She did not want to do this, but they were here on her doorstep, and knowing them, they would not leave until they had seen her.

 _Let them into the camp,_ she instructed. She had a feeling that the rest of her day was going to be unpleasant, to say the least.

* * *

Much to their surprise, the crew of the Replicator ship informed them that their commander was not onboard their ship, but was down in their camp on the planet. They freely gave Labrea permission to go down, and that “Commander Weir” would await them.

John offered the use of the puddlejumper they had brought with them, and the trip only took a few minutes. As they walked the small distance across a field toward the camp, he quickly took in his surroundings. The camp resembled one of their alpha sites, with a few almost ramshackle buildings and stockpiles of large crates piled neatly here and there. The Stargate was in the center, guarded by three figures and with a machine attached to it by cables. A device that let them control the Gate’s use, maybe?

They were met by a man dressed in the normal white clothes associated with the Replicators, the off-white bodysuits. John couldn’t help but stiffen as the man examined them closely for several moments, not saying anything. He had a feeling that they had been recognized, and found wanting. It wasn’t a comfortable experience.

“Captain Labrea,” the man said, “you are most welcome. We were not expecting you for another two weeks.” His eyes were still on John.

“I know, Lincone,” Labrea replied, “and I’m sorry for the unexpected drop-by. But these people are allies of my people, and they have a great desire to speak with Commander Weir as soon as possible.” She gestured to John. “This is –”

“I am aware of their identities, Captain,” Lincone interrupted, his eyes a frosty blue. “Colonel John Sheppard, Doctor Rodney McKay, Ronon Dex, and Teyla Emmagan, all of Atalantë.”

John blinked at the unfamiliar, though still recognizable, term for Atlantis, but didn’t let it distract him. He didn’t bother beating around the bush either. “Is Elizabeth here?” he demanded.

If anything, Lincone’s expression became even more severe. “ _Commander Weir_ ,” he stressed, “is in camp. She has already expressed her permission to allow you into camp. She will be happy to see Captain Labrea. As for the rest of you…” He didn’t need to complete the sentence. His thoughts were perfectly clear.

John gritted his teeth. He’d been running pretty much on autopilot for the past three days, focusing on getting to Elizabeth, on seeing her and asking her to come home. He really wanted nothing more than to brush this guy aside and tear the place apart until he found her. Not to mention, the man’s attitude was about as grating as Rodney’s was before his third up of coffee in the morning.

Luckily, Teyla took over at that point. She probably saved them from getting summarily tossed from the camp. The picture of poise, she said, “We had been unaware that… Commander Weir… was still alive, having been informed that the leader of the Replicators had had her killed. Her abrupt arrival shocked many of us, and we were unable to thank her properly for her assistance against the Wraith.”

* * *

 _The Athosian leader claims to not know that you were alive, Commander. Orders?_

 _Bring them to me, Lincone,_ she ordered, steeling herself for what was to come.

* * *

Lincone’s disapproving expression didn’t change much even after Teyla’s intervention, but he abruptly straightened, like someone had just cracked a whip. “Follow me,” he ordered, turning on his heel.

Labrea stepped back. “I think you four should go ahead,” she told them. “My business with the commander can wait.”

John didn’t argue with her, just hurried after Lincone. The man – Replicator? – led him and the others to one of the smaller buildings and knocked on the door. Sheppard’s breath caught when he heard a voice call from the other side, “Come in.”

Lincone opened the door and stepped into the doorway. “The team from Atalantë as you requested, Commander,” he said.

“Good. Thank you, Lincone.”

The man turned and after giving them one final glare, he strode away. John swallowed with difficulty, and then led his team into the building.

The building, to be honest, wasn’t all that large. From what he could tell, it was two, maybe three, rooms in all, the office-area that they were standing in, and what lay beyond the other doorway. Still, John really didn’t care. His eyes had fallen on the figure seated behind the desk. A woman with familiar green eyes and dark curls framing her face.

A woman in very cool black and red leather.

For several seconds, no one broke the silence. John stared at Elizabeth and was pretty sure Teyla, Ronon, and Rodney were staring at her too. Elizabeth, for her part, just stared back at them, her expression revealing nothing. Then, “I didn’t expect you to be here.”

John blinked rapidly, but then replied, “Uh, yeah. You left before we could give you the ‘thanks for saving our asses’ cake.”

His stupid jokes had always made her smile before, or at least roll her eyes. Now, her face didn’t even flicker the slightest bit. She just stared at him.

“Elizabeth,” Teyla interjected before he could say something even more stupid, “we were not aware that you had survived. We’d been informed that you had been killed on Oberoth’s orders.”

She shrugged. “I’m sure he intended to eventually, but thanks to some timely intervention, he had bigger issues to deal with. I was… reprogrammed and sent on my way. It didn’t work out as well as he hoped.”

Reprogrammed. John cringed inwardly. He could imagine what that entailed, had seen the results of “reprogramming” more than once in his career. He barely noted the choked sound coming from Rodney.

Elizabeth paused, cocking her head a bit as though she was listening to someone else speak. After a moment, she then said, “I have several things to do before I meet with Captain Labrea. If you’d like to speak to me later, I can arrange something.”

It was a dismissal, loud and clear. She wanted them out of her office. John didn’t have to turn to see the flash of hurt cross Teyla’s features, or the kicked puppy look on Rodney’s, or the sulky one on Ronon’s. It was enough to whip him out of the trance-like state he’d been in. Now he was pissed.

 _Why is she acting like this? To_ us, _of all people?_

John motioned for the others to go outside, but remained behind himself, watching as Elizabeth stared intently at something on the monitor stationed on her desk. A few seconds later, she looked up, irritated. “Colonel, I believe I said I would speak to you later –”

“Enough with the diplomatic bullshit, Elizabeth,” he snapped at her. “What the _hell_ is your problem?”

Her eyes narrowed. “I don’t know what you’re talking about.”

“Then let me enlighten you. You show up out of nowhere, blow a Wraith hive ship that’s bent on killing us to high hell, and then take off for parts unknown with barely a ‘hi, see you later.’ Never mind the hell we went through –”

That last part was apparently the wrong thing to say. Elizabeth’s restrained irritated look was gone in that instant, replaced by flashing eyes and rapidly-reddening cheeks. The last time John had seen _that_ look was when she chewed McKay’s ass off for blowing up three-quarters of a solar system.

“The hell _you_ went through.” The words came out as a snarl. Elizabeth _snarled_. It was scary. “You want to talk about the hell you went through, John? You were all safe on Atlantis, hidden away where the Replicators would have a very hard time ever finding you again. You were back in contact with Earth, with all the resources that entails at your disposal.”

The fist she slammed down on her desk might have made someone else jump, but John just stared at her, let her rant.

“Now,” she continued, her voice frigid, “let’s talk about _my_ hell. I am left behind to deal with the Replicators so you can get the ZPM back to Atlantis, just as I ordered. I am taken prisoner, strapped to a gurney, and railed at for several hours by Oberoth. He swears eternal vengeance, that he’ll destroy my city and make me watch as he kills the entire expedition. However, since that’s currently beyond his capabilities _for the moment_ , he figures it’s best to give me a warm up.”

Her eyes were cold as she continues her recitation. “He sticks his hand in my head, forces me to deal with my worst nightmares, over and over again. What the nanites did to me before was a pleasantry in comparison to what Oberoth did to me. Of course, he couldn’t do it to me _all_ the time. He had other duties to perform, now that Rodney had restarted their programming to attack the Wraith. I became his pet project, his hobby, his way to take a break from the stresses of leadership.”

John was pretty sure his blood was turning to ice in his veins, but Elizabeth didn’t seem inclined to stop now.

“When Oberoth wasn’t fucking my brain six ways to Sunday, I waited. I remembered the phrase _‘you don’t leave your people in the hands of the enemy.’_ I was certain that at any moment, you, Ronon, and Teyla were going to come busting through the door to pull me out.” She laughed bitterly, which sent yet another chill through John’s bones. “When Oberoth found that particular thought in my head, he used it for his own amusement with great… relish. Had the three of you rushing to my rescue only to be unceremoniously slaughtered on the way out. That was one of his favorite scenarios.”

Elizabeth paused again, and then crossed her arms. “Days turned into weeks, and some of the survivors of Niam’s group began to talk to me when they could. They were beginning to see the pragmatics of their situation. They still had no desire to follow Oberoth into waging a bloody war throughout the galaxy, but neither did they think that Ascension was the answer to their problems like Niam and his closest followers had. That was when I began to be pragmatic too. You weren’t coming. There would be no rescue. I was on my own.”

Her voice dropped to an angry whisper. “So don’t talk to _me_ about hell, John Sheppard. I know it very well, what it is to be let down by those you count on.”

John really had no idea what to say to her. He’d had nightmares in the aftermath of that entire disaster, his brain conjuring up all sorts of horrors that the Replicators would put her through. Though he’d known that Sam was right when she told him that he needed a rescue plan that actually had a little more than a snowball’s chance in hell of succeeding, it hadn’t been a comfort then and looking into Elizabeth’s angry green eyes, it wasn’t a comfort now. So he had lived with the guilt of breaking the cardinal rule that every person in the military had beaten into them from the beginning: you don’t leave your people behind when the shit hits the fan. He had kept going, because that was what he knew how to do, and John had taken great pleasure in watching the Replicator world collapse in on itself, imaging that Oberoth was dying a very painful death.

The son-of-a-bitch had killed her, and then he paid for it. Except that she hadn’t died. She was right here.

“We thought you were dead,” he blurted out. “These Replicators, clones of us, they’d been told that you were dead, that Oberoth had killed you. They –”

“And you _believed_ them?” Elizabeth snapped. “Since when do we take the word of the enemy at face value, Colonel? When the Genii call and ask us for a favor, do we simply just assume they have good intentions?”

Yet again, she was right. They hadn’t bothered to check the Replicators’ story on Elizabeth, hadn’t tried to scan for a human life-sign when they attacked their homeworld. John had just tried to make the best of the fact that she was at peace, that nothing could hurt her anymore now.

Until she decided to show up in a Replicator ship, blow a Wraith ship to hell, and dart out like she’d never been there. From that point on, John had been consumed with finding her, with bringing her back home, just so he’d have one less regret on his heart. Maybe that was the problem right there. He had been so consumed with alleviating _his_ guilt, he hadn’t really considered what she might be feeling.

That thought was like a punch in the gut.

“I’m sorry,” John whispered.

“What?”

“I’m sorry,” he repeated, more strongly this time. “We should have come back for you, should have tried harder to find a way…”

Much to his surprise, some of the anger seemed to leave Elizabeth’s face and she waved her hand. “What’s done is done,” she told him. “The question now remains: what now? Are you going to go back to Atlantis and tell them where we are so they can send Stephen on the _Daedalus_ to destroy us? Because there is no need. We all of us here are human, though we do have nanites in our bloodstream to assist in basic functions like accelerated healing. Their programming to spread to other beings has been deactivated.”

John blinked. That thought hadn’t even crossed his mind, but he knew that it was a possibility once the IOA got in on this. They might decide that Elizabeth and her crew were a liability. “We don’t know the coordinates of this planet,” he reminded her. “Labrea brought us here.”

“Good. I really don’t want to have to pack up just yet.”

He nodded, but couldn’t think of anything else to say. Really, what could be said at this point? Elizabeth had changed so much that it almost hurt to look at her. He kept remembering the woman from _before_ , who had loved Atlantis so much that she could never let go of it, who worked too hard most of the time and had to be reminded by Carson numerous times to eat and sleep, who enjoyed a piece of apple pie when she thought no one was looking, who smiled a kind of smile at him that made his knees go weak –

John shook that thought off. It wasn’t the time for it, if there ever _would_ be a time for it. “You’re taking out Wraith ships, right?” he asked. At her nod, he continued. “Maybe we can help each other, get you supplies in exchange for information or something.”

Elizabeth stared at him, and he thought he saw a flicker of some kind of emotion on her face, but he couldn’t be sure. “An alliance?” she asked.

“Yeah, why not?”

She didn’t respond at first, just stared at him. Then, much to his surprise, she started to laugh. It wasn’t the same laugh he had known on Atlantis, it was far too bitter.

“You don’t make things easy, John,” she said. “The IOA will pitch a _fit_ when they hear that idea.”

She wasn’t his Elizabeth, wasn’t the woman he had known. It _hurt_ , admitting that. Still, she was here, still doing what she could to make a difference. It wasn’t what John wanted, and he doubted it was what she had wanted.

He didn’t want to leave it like this, but he didn’t think he had a choice, really. Some things just couldn’t be fixed over the course of one argument. If he wanted any chance of trying to make things right again, John would have to convince her.

He’d do his best. It was all he could offer her.


End file.
